File1

A    apple
B    banana
C    citrus

File2

A    red
B    yellow
C    orange

program.pl File1 File2

A    apple    red
B    banana    yellow
C    citrus    orange

foreach line in ARGV[0]
    split the line by tabs
    assign key and value

foreach line in ARGV[1]
    split the line by tabs
    assign key and value

for each key from ARGV[0]
    print key, value, ARGV[1](key)

  1 #!/usr/bin/perl -w
  2 use diagnostics;
  3 use warnings;
  4 
  5 %affyMap = ();
  6 %affyAnnot = ();
  7 @map = <$ARGV[0]>;
  8 @annotation = <$ARGV[1]>;
  9 $line = "";
 10 
 11 foreach $line (@map){
 12         chomp($line);
 13         my($ID,$info) = split(/\t/,$line,2);
 14         $affyMap{$ID} = $info;
 15 }
 16 
 17 foreach $line (@annotation){
 18         chomp($line);
 19         my($ID,$info) = split(/\t/,$line,2);
 20         $affyAnnot{$ID} = $info;
 21 }
 22 
 23 foreach $key (%affyMap){
 24         print "$key\t" . "$affyMap{$key}\t" . "$affyAnnot{$key}\n";
 25         }